Genetic Code And Protien Synthesis Flashcards
What is the genetic code
Which way is it read
3 nucleotide sequences in the mRNA that form amino acids
Universal
These are read from 5’ to 3’ in the mRNA
What is degeneracy in the genetic code
What are synonymous codons
More than one codon (three letter sequence) codes a specific AA
They are the codons that are all different but code for the same AA
What is codon bias
When an organism prefers one specific type of codon to code and AA
rather than another codon that codes the exact same thing
What are the start codons
Stop codons
AUG
UAA, UAG, UGA
What type of molecules are tRNA
Adaptor molecules
(Link multiple protiens together)
What is the structure of tRNA
Small
L shaped
5’ end is phosphorylated and has and anticodon loop (where it base pairs with rna codon)
3’ end has a CCA component where the amino acid is attached
tRNA’s have modified bases that base pair with the mRNA
what is one and how is it formed
Inosine
It’s made when adenosine (adenine base and a sugar) is deaminated
If just adenine deaminated it’s hypoxanthine
Why is it important for tRNA to have a modified base like inosine
What bases can inosine pair with
Because it is able to do wobble base pairing where one tRNA codon is able to recognize more than one codon in the mRNA
Inosine is in the third position of the anticodon and can pair with C U AND A
How does inspire helping in wobble base pairing show degeneracy in the genetic code
Since the specific TRNA anticodon with Inosine can bind to many diff mRNA codons, the same amino acid is made for those many codons
What is tRNA charging
It involves the 3’ CCA arm
amino acids are added to the tRNA CCA arm
Why does the tRNA have to be activated first before starting translation and making proteins
Because forming peptide bonds between free amino acids is thermodynamically unfavourable
What is the activated intermediate of tRNA
What is it called
The activated intermediated is an amino acid ester
It’s called aminoacyl tRNA
How is the amino acids to be added to the 3’ end of the tRNA activated
By the adenylation (adding adenines) of the amino acids
After the amino acid for tRNA charging is activated what does it turn into and where does it go
It turns into aminoacyl-AMP and is transferred to the tRNA 3’ end
What catalyzes the adenylation of the amino acid and the transfer of it to the tRNA
Aminoacyl tRNA synthetase
This is what ultimately makes the charged tRNA
What is the first activation by adenylation step of tRNA charging
What makes the amino acid actually get activated
This is where the carboxy group of the amino acid attacks the alpha phosphate of the atp (adenylate)
This releases PPi and makes aminoacyl-AMP
The amino acid is now activated by the phosphoester bond between the AA and the phosphate of the amp
What is the 2nd transfer to tRNA step of tRNA charging
What charges the tRNA
The 3’ oh of the Adenine of the 3’ CCA of the tRNA attacks the caboxy group of the amino acid in the amino acyl amp
This releases amp and forms aminoacyl- tRNA
The ester linkage of the 3’ OH of the adenosine from CCA and the amino acid charges the tRNA
What does the aminoacyl tRNA synthetase do in tRNA charging
It bind to the tRNA and AA and ATP
This allows all the reactions to happen to make the charge tRNA
Because each aminoacyl tRNA synthetase is specific to only one amino acid that it adds to the tRNA
What is an example of something that could get mixed up
Example. If threonyl-tRNA synthetase want threonine (oh side group with methyl)
But valine (ch3 side group) and serine (oh but no methyl) are similar to threonine
Need to find a way to get only thr and not Val or ser
How does threonyl - tRNA synthetase make sure valine does not get mixed up with threonine
It all depends on the zinc in the active site of the enzyme.
The Val side chain methyl prevents interaction with the enzymes active zinc because it’s not an oh
So it doesn’t get attached to the enzyme
How does threonyl - tRNA synthetase make sure serine does not get mixed up with threonine
Since the serine also has an OH, it can attach to the activation site zinc of the enzyme.
This means it does get attached to the tRNA
But the enzyme has an editing site where the serine can’t fit into because of it doesn’t have the extra methyl group that the does
So it doesn’t stay in the tRNA
What is the ribosome made up of
ribosomal rna and protiens
It has a 30s subunit and 50s subunit to make up the 70s ribosome
It has the E P A three binding sites for tRNA in the ribosome
What does E P A stand for
Exit
Peptidyl
Amino acyl
What is the direction of translation?
On the 5’-3’ mRNA the ribosome moves in a 5’-3’direction on the mRNA
How is translation initiated in bacteria by forming the 30s initiation complex
First the 30s unit of the ribosome forms a complex with IF1 and 3 (initiation factors)
This makes it so the the 30s doesn’t prematurely bind to the 50s subunit
Then the IF2 binds to GTP and then to fMET trna (the thing that adds fMET)
This if2 GTP F met tRNA binds to the mRNA AUG and the 30s subunit to make the 30s initiation complex
When the 30s initiation complex is made, what happens
The 70s initiation complex is formed by IF1 and 3 leaving the 30s subunit
This causes the 50s subunit to come to the 30s subunit
Once the 50s subunit arrives, the GTP on IF2 is hydrolyzed and IF2 leaves
This forms the 70s initiation complex where the fMET tRNA is at the p site
How does elongation occurs once the ribosome has been created on the start codon
EF-Tu-GTP binds to aminoacyl-tRNAs and moves them to the A site of the ribosome
If the base pairing is right, the EF-Tu hydrolyzes GTP to gdp and releases the aminoacyl tRNA to the A site
What does Ef-Tu-GTP protect
The ester linkage in the aminoacyl tRNA
Once both the A site and the P site are occupied by aminoacyl tRNAs what happens
Need to make a peptide bond between the two AA
The fMET carboxy group on the P site initiatior tRNA gets attacked by the amino group of the amino acid on the A site tRNA
This means the new peptide bonds are formed on the tRNA in the A site
Once a peptide bond is forms and the two amino acids are on the A site MRNA, what happens
Where does each thing go
Translocation occurs
The mRNA along with tRNA attached to it shifts over to the 5’ end by three nucleotides
This makes it so that the next three nucleotides (codon) are in the A site.
The tRNA with the growing chain moves to the P site and the fMET tRNA move to the e site
During translocation, how does the MRNA actually move to the left by three nucleotides
EF-G near the A site bind and hydrolyzes GTP and pushes the mRNA and tRNA to the left by one codon
How is termination done
RF1 or 2 protiens recognize the stop codons and bind at the A SITE stop codon
Once bound, they hydrolyze the last ester linkage between the peptide and the TRNA in the p site
This release the peptide
After the peptide is released in termination, what can happens to it
It can be post translationally modified
After the peptide is gone due to termination how does RF1 or RF2 leave
How is the ribosome disassembled
Rf3-GTP hydrolyzes GTP and indirectly makes RF1 or RF2 leave the mRNA
EF-G hydrolyzes GTP and triggers the ribosome to disassemble
What are the enzymes that hydrolyze atp of GTP in
TRNA charging
Initiation
Elongation
Termination
Trna charging: aminoacyltrnasynthestase (ATP)
Initiation: IF2 (GTP)
Elongation: EF-Tu (GTP), EF-G (GTP)
Termination: RF3 (GTP), EF-G (GTP)
What are the most commonly modified amino acid side chains in post translation modification
How can they be modified
Ones with OH, amino or Thiol functional groups
Ex. Ser/thr with OH side chain can be phosphorylated or glycosylated
What is the effect of postranslational modification?
It influences the chemical properties of the protien
Changes the net charge
Changes the confirmation
Changing the binding/function
Is postranslational modification reversible?
Is it specific
Yes
Yes a specific enzyme catalyzes each modification
Which protien is commonly changed by lipidation
Phosphorylation
Glycosylation
Things with Thiol groups like cysteine
Things with oh like serine or threonine
Thins with nh2 like aspargine
